Mass spectrometry (MS) and, in particular, tandem mass spectrometry (MS/MS) coupled with a chromatographic separation technique such as liquid chromatography (LC) or gas chromatography (GC) has found widespread application in the analytical sciences due its high sensitivity, selectivity, and throughput. Commercial instruments typically employ calibrations that help to optimize various parameters such as MS/MS collision energy as a function of characteristics of anticipated analytes such as mass and charge. Each such calibration is only highly successful for a narrow class of analytes, such as peptides. For classes of analytes other than the class for which a particular calibration was developed, the calibration may be much less successful, due to the disparate compound structures and cleavable bonds that may be encountered. Thus, for analysis of many species such as drug compounds, pesticides, and metabolites, targeted methods must be painstakingly developed through a process of manual optimization for each class of compound or more commonly for each individual compound. A typical pesticide assay of 300 compounds, for example, is conventionally developed by producing sets of mixtures of ˜10 compounds each. Each of the 30 mixtures is separately infused with a syringe pump into a mass spectrometer, and the mass spectrometer parameters of interest are optimized for each compound in the mixture. Even when performed by a trained analyst, this process requires a time duration on the order of 1-2 weeks to complete. Strides are being made towards automating parts of this process; for example, an autosampler can be used to infuse the compounds. Nonetheless, the key limitation has not yet been addressed, which is the need to create many subsets of compounds and infuse each one separately. One important problem that must be overcome in order to address this limitation is that the current optimization techniques are not able to account for analyte flux that varies with time; as a result, the improved efficiency that hypothetically could be achieved by LC separation is not available for such optimization programs. The present inventor has thus recognized a need in the mass spectrometry art for development of more-efficient methods of optimizing mass spectrometer operational parameters that may be employed on chromatography fractions as they elute. This disclosure provides methods that remedy this problem, enabling MS parameter optimization on mixtures of large numbers of compounds in a shorter amount of time than is required using conventional techniques.